In order to characterize the stable association between host cell DNA and viral sequences, molecular clones of several newly integrated retroviral genomes were produced in either plasmid or bacteriophage cloning vehicles using approved recombinant DNA techniques and were extensively studied using electron microscope heteroduplex methods. Retroviruses provide a unique and important system for such studies since exogenously acquired genomes are integrated at a specific site in the viral genome, but at a large number of sites in cellular DNA. The major objective of these studies has been the application of physical and biochemical techinques to assess the influence of flanking cellular sequences on subsequent viral function and to define in molecular terms these events which take place during integrative recombination.